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musharna

plant-genomics-mcp

by musharna

Batch: Gene Cross-References

batch_get_gene_xrefs
Read-onlyIdempotent

Retrieve cross-references (xrefs) for up to 50 plant gene loci at once from Ensembl Plants. Each locus returns its xref count, list, and rollup by database.

Instructions

Batch variant of get_gene_xrefs. Fans out per-locus xref lookups over Ensembl Plants in parallel (up to 50 loci). Each results[locus] is the full single-locus shape (count + xrefs[] + by_db rollup).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYesList of locus identifiers (1–50). Successes land in results[locus]; PlantGenomicsError failures in errors[locus].
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
toolYesThe batch tool name, e.g. batch_resolve_locus_to_uniprot
countYesNumber of distinct loci queried, returned (== len(results) + len(errors)). The input list is de-duplicated first, so this is LOWER than the number of loci you sent if you sent a duplicate — that is de-duplication, not a dropped locus.
errorsYeslocus → '[ClassName] message' for PlantGenomicsError failures
resultsYeslocus → per-locus result dict (same shape as the single-locus tool)
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already indicate read-only, idempotent, open-world, non-destructive behavior. The description adds valuable context: parallel fan-out, 50-locus limit, and the output structure per locus. No contradictions with annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two sentences with no wasted words. It front-loads the core identity ('Batch variant of get_gene_xrefs') and then details behavior concisely.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the presence of full annotations and an output schema, the description is complete. It covers the batch nature, parallelism, limits, and output shape. No critical missing information for effective tool use.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so baseline is 3. The description does not add meaning beyond the schema; it mentions the loci parameter implicitly but does not elaborate on organism. The parameter semantics are adequately covered by the input schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly identifies this as a batch variant of get_gene_xrefs, describes the parallel fan-out over Ensembl Plants with a max of 50 loci, and specifies the output shape per locus. It effectively distinguishes this tool from the single-locus version.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implicitly suggests use for multiple loci, but lacks explicit guidance on when to use this vs alternatives (e.g., the single-locus get_gene_xrefs or other batch tools). No when-not-to-use or alternative mentions are provided.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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